Count data instead of normalized relative abundance

[Muntsa Rocafort]

Hello,

I am quite new using Metaphlan2 and I would like to know if there is any way using Metaphlan2 to get the biom file with count data instead of normalized relative abundance. In a previous post someone asked a similar question but the answer given did not work for me as the count_marker option does not seem to exist.

I just need to be able to calculate richness and diversity using R phyloseq package but it does not accept non-integers values (i.e. relative abundances).

Thank you

[Nicola Segata]

Hi Muntsa,

 because of how MetaPhlAn works (i.e. by estimating the coverage on marker genes), count data cannot be natively supported. But with the biom or abundance file, what you can do is to multiply all the values for, say, 1M and convert them to integer numbers. As long as the richness and diversity measure you use are scale-invariant, this will do the trick.

I hope it helps

Nicola

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